Package: SwathXtend

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SwathXtend_2.9.0.tar.gz

StartedAt: 2020-01-16 09:21:01 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:24:20 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 199.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SwathXtend.Rcheck

Warnings: 1

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SwathXtend_2.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SwathXtend.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SwathXtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwathXtend’ version ‘2.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SwathXtend’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 351.5Mb
  sub-directories of 1Mb or more:
    files  351.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
  ds.seed$Peptide, extSwath = ds.ext$Peptide), file = "venn of
  peptide.png", category.names = c("seed", "extended"), fill =
  c("aquamarine1", "chartreuse"), main = paste("Peptides at FDR pass",
  nfdr)): partial argument match of 'file' to 'filename'
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
  ds.seed$Protein, extSwath = ds.ext$Protein), file = "venn of
  protein.png", category.names = c("seed", "extended"), fill =
  c("aquamarine1", "chartreuse"), main = paste("Proteins at FDR pass",
  nfdr)): partial argument match of 'file' to 'filename'
alignRTbyHydro: no visible global function definition for ‘as.formula’
alignRTbyHydro: no visible global function definition for ‘lm’
alignRTbyHydro: no visible global function definition for ‘predict’
applyttest : <anonymous>: no visible global function definition for
  ‘t.test’
applyttest : <anonymous>: no visible global function definition for
  ‘na.omit’
applyttestPep : <anonymous>: no visible global function definition for
  ‘na.omit’
applyttestPep: no visible global function definition for ‘aggregate’
applyttestPep : <anonymous>: no visible global function definition for
  ‘t.test’
checkQuality: no visible global function definition for ‘median’
computeRIICor : <anonymous>: no visible global function definition for
  ‘cor’
computeRIICor: no visible global function definition for ‘data’
computeRIICor: no visible global function definition for ‘png’
computeRIICor: no visible global function definition for ‘boxplot’
computeRIICor: no visible global function definition for ‘abline’
computeRIICor: no visible global function definition for ‘dev.off’
computeRTCor: no visible global function definition for ‘cor’
computeRTCor: no visible global function definition for ‘predict’
computeRTCor: no visible global function definition for ‘png’
computeRTCor: no visible global function definition for ‘plot’
computeRTCor: no visible global function definition for ‘lines’
computeRTCor: no visible global function definition for ‘lowess’
computeRTCor: no visible global function definition for ‘text’
computeRTCor: no visible global function definition for ‘dev.off’
computeRTCor: no visible global function definition for ‘abline’
computeRTCor: no visible global function definition for ‘axis’
computeRTCor: no visible global function definition for ‘as.formula’
computeRTCor: no visible global function definition for ‘lm’
computeRTCor: no visible global function definition for ‘layout’
computeRTCor: no visible global function definition for ‘resid’
computeRTCor: no visible global function definition for ‘residuals’
cv: no visible global function definition for ‘sd’
cv: no visible global function definition for ‘na.omit’
fdr.crit : <anonymous>: no visible global function definition for
  ‘na.omit’
medianNorm : <anonymous>: no visible global function definition for
  ‘median’
medianNorm : <anonymous>: no visible global function definition for
  ‘na.omit’
mlr: no visible global function definition for ‘na.omit’
mlr: no visible global function definition for ‘hist’
mlr: no visible global function definition for ‘density’
mlr: no visible global function definition for ‘lines’
mlr: no visible global function definition for ‘abline’
mlr: no visible global function definition for ‘text’
mlr: no visible global function definition for ‘segments’
mlrrep: no visible global function definition for ‘na.omit’
normalise: no visible global function definition for ‘aggregate’
outputLib: no visible global function definition for ‘write.table’
parseAccession: no visible global function definition for ‘na.omit’
plotDensities: no visible global function definition for ‘rainbow’
plotDensities: no visible global function definition for ‘density’
plotDensities: no visible global function definition for ‘plot’
plotDensities: no visible global function definition for ‘lines’
plotDensities: no visible global function definition for ‘legend’
plotErrorBarsLines: no visible global function definition for ‘par’
plotErrorBarsLines: no visible global function definition for ‘plot’
plotErrorBarsLines: no visible global function definition for ‘axis’
plotRIICor : <anonymous>: no visible global function definition for
  ‘cor’
plotRIICor: no visible global function definition for ‘data’
plotRIICor: no visible global function definition for ‘boxplot’
plotRIICor: no visible global function definition for ‘abline’
plotRTCor: no visible global function definition for ‘cor’
plotRTCor: no visible global function definition for ‘predict’
plotRTCor: no visible global function definition for ‘plot’
plotRTCor: no visible global function definition for ‘lines’
plotRTCor: no visible global function definition for ‘lowess’
plotRTCor: no visible global function definition for ‘text’
plotRTResd: no visible global function definition for ‘predict’
plotRTResd: no visible global function definition for ‘plot’
plotRTResd: no visible global function definition for ‘abline’
plotRTResd: no visible global function definition for ‘axis’
plotRTResd: no visible global function definition for ‘text’
plotRelativeDensities: no visible global function definition for
  ‘rainbow’
plotRelativeDensities: no visible global function definition for ‘plot’
plotRelativeDensities: no visible global function definition for
  ‘density’
plotRelativeDensities: no visible global function definition for
  ‘na.omit’
plotRelativeDensities: no visible global function definition for
  ‘abline’
plotRelativeDensities: no visible global function definition for
  ‘lines’
plotStats: no visible global function definition for ‘png’
plotStats: no visible global function definition for ‘layout’
plotStats: no visible global function definition for ‘barplot’
plotStats: no visible global function definition for ‘dev.off’
plotStats: no visible global function definition for ‘plot’
plotStats: no visible global function definition for ‘density’
plotStats: no visible global function definition for ‘abline’
plotStats: no visible global function definition for ‘aggregate’
plotStats: no visible global function definition for ‘hist’
plotStats: no visible global function definition for ‘par’
predictRT: no visible global function definition for ‘cor’
predictRT: no visible global function definition for ‘lm’
predictRT: no visible global function definition for ‘predict’
quantification.accuracy: no visible global function definition for
  ‘cor’
quantification.accuracy: no visible global function definition for
  ‘median’
readLibFile: no visible global function definition for ‘read.delim2’
reliabilityCheckLibrary: no visible global function definition for
  ‘read.delim’
reliabilityCheckLibrary: no visible global function definition for
  ‘png’
reliabilityCheckLibrary: no visible global function definition for
  ‘barplot’
reliabilityCheckLibrary: no visible global function definition for
  ‘gray’
reliabilityCheckLibrary: no visible global function definition for
  ‘axis’
reliabilityCheckLibrary: no visible global function definition for
  ‘points’
reliabilityCheckLibrary: no visible global function definition for
  ‘mtext’
reliabilityCheckLibrary: no visible global function definition for
  ‘par’
reliabilityCheckLibrary: no visible global function definition for
  ‘legend’
reliabilityCheckLibrary: no visible global function definition for
  ‘dev.off’
reliabilityCheckLibrary: no visible global function definition for
  ‘write.csv’
reliabilityCheckSwath: no visible global function definition for
  ‘flog.threshold’
reliabilityCheckSwath: no visible binding for global variable ‘ERROR’
reliabilityCheckSwath: no visible global function definition for ‘png’
reliabilityCheckSwath: no visible global function definition for
  ‘layout’
reliabilityCheckSwath: no visible global function definition for ‘plot’
reliabilityCheckSwath: no visible global function definition for
  ‘density’
reliabilityCheckSwath: no visible global function definition for
  ‘dev.off’
reliabilityCheckSwath: no visible global function definition for
  ‘gray.colors’
reliabilityCheckSwath: no visible global function definition for ‘par’
reliabilityCheckSwath: no visible global function definition for
  ‘barplot’
reliabilityCheckSwath: no visible global function definition for
  ‘legend’
reliabilityCheckSwath: no visible global function definition for
  ‘terrain.colors’
reliabilityCheckSwath : <anonymous>: no visible global function
  definition for ‘aggregate’
reliabilityCheckSwath: no visible binding for global variable ‘median’
reliabilityCheckSwath: no visible global function definition for
  ‘boxplot’
reliabilityCheckSwath: no visible global function definition for
  ‘write.csv’
selectModel: no visible global function definition for ‘as.formula’
selectModel: no visible global function definition for ‘predict’
selectModel: no visible global function definition for ‘lm’
swath.means: no visible global function definition for ‘aggregate’
swath.means : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  ERROR abline aggregate as.formula axis barplot boxplot cor data
  density dev.off flog.threshold gray gray.colors hist layout legend
  lines lm lowess median mtext na.omit par plot png points predict
  rainbow read.delim read.delim2 resid residuals sd segments t.test
  terrain.colors text write.csv write.table
Consider adding
  importFrom("grDevices", "dev.off", "gray", "gray.colors", "png",
             "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
             "layout", "legend", "lines", "mtext", "par", "plot",
             "points", "segments", "text")
  importFrom("stats", "aggregate", "as.formula", "cor", "density", "lm",
             "lowess", "median", "na.omit", "predict", "resid",
             "residuals", "sd", "t.test")
  importFrom("utils", "data", "read.delim", "read.delim2", "write.csv",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: applyttest.Rd:27-28: Dropping empty section \details
prepare_Rd: applyttest.Rd:36-37: Dropping empty section \note
prepare_Rd: applyttest.Rd:34-35: Dropping empty section \author
prepare_Rd: applyttest.Rd:32-33: Dropping empty section \references
prepare_Rd: applyttestPep.Rd:26-27: Dropping empty section \details
prepare_Rd: applyttestPep.Rd:35-36: Dropping empty section \note
prepare_Rd: applyttestPep.Rd:33-34: Dropping empty section \author
prepare_Rd: applyttestPep.Rd:31-32: Dropping empty section \references
prepare_Rd: coverage.Rd:7-9: Dropping empty section \description
prepare_Rd: coverage.Rd:35-37: Dropping empty section \note
prepare_Rd: coverage.Rd:32-34: Dropping empty section \author
prepare_Rd: coverage.Rd:29-31: Dropping empty section \references
prepare_Rd: coverage.Rd:41-43: Dropping empty section \seealso
checkRd: (5) coverage.Rd:0-51: Must have a \description
prepare_Rd: cv.Rd:7-9: Dropping empty section \description
prepare_Rd: cv.Rd:19-21: Dropping empty section \details
prepare_Rd: cv.Rd:31-33: Dropping empty section \note
prepare_Rd: cv.Rd:28-30: Dropping empty section \author
prepare_Rd: cv.Rd:25-27: Dropping empty section \references
prepare_Rd: cv.Rd:37-39: Dropping empty section \seealso
checkRd: (5) cv.Rd:0-48: Must have a \description
prepare_Rd: fdr.crit.Rd:7-9: Dropping empty section \description
prepare_Rd: fdr.crit.Rd:19-21: Dropping empty section \details
prepare_Rd: fdr.crit.Rd:22-28: Dropping empty section \value
prepare_Rd: fdr.crit.Rd:35-37: Dropping empty section \note
prepare_Rd: fdr.crit.Rd:32-34: Dropping empty section \author
prepare_Rd: fdr.crit.Rd:29-31: Dropping empty section \references
prepare_Rd: fdr.crit.Rd:41-43: Dropping empty section \seealso
checkRd: (5) fdr.crit.Rd:0-63: Must have a \description
prepare_Rd: getFdrBins.Rd:7-9: Dropping empty section \description
prepare_Rd: getFdrBins.Rd:22-24: Dropping empty section \details
prepare_Rd: getFdrBins.Rd:34-36: Dropping empty section \note
prepare_Rd: getFdrBins.Rd:31-33: Dropping empty section \author
prepare_Rd: getFdrBins.Rd:28-30: Dropping empty section \references
prepare_Rd: getFdrBins.Rd:40-42: Dropping empty section \seealso
checkRd: (5) getFdrBins.Rd:0-59: Must have a \description
prepare_Rd: medianNorm.Rd:17-18: Dropping empty section \details
prepare_Rd: medianNorm.Rd:26-27: Dropping empty section \note
prepare_Rd: medianNorm.Rd:24-25: Dropping empty section \author
prepare_Rd: medianNorm.Rd:22-23: Dropping empty section \references
prepare_Rd: medianNorm.Rd:30-31: Dropping empty section \seealso
prepare_Rd: mlr.Rd:20-21: Dropping empty section \details
prepare_Rd: mlr.Rd:32-33: Dropping empty section \note
prepare_Rd: mlr.Rd:30-31: Dropping empty section \author
prepare_Rd: mlr.Rd:36-37: Dropping empty section \seealso
prepare_Rd: mlrGroup.Rd:20-22: Dropping empty section \details
prepare_Rd: mlrGroup.Rd:31-32: Dropping empty section \note
prepare_Rd: mlrGroup.Rd:29-30: Dropping empty section \author
prepare_Rd: mlrrep.Rd:17-18: Dropping empty section \details
prepare_Rd: mlrrep.Rd:29-30: Dropping empty section \note
prepare_Rd: mlrrep.Rd:27-28: Dropping empty section \author
prepare_Rd: mlrrep.Rd:25-26: Dropping empty section \references
prepare_Rd: plotDensities.Rd:23-24: Dropping empty section \details
prepare_Rd: plotDensities.Rd:32-33: Dropping empty section \note
prepare_Rd: plotDensities.Rd:30-31: Dropping empty section \author
prepare_Rd: plotDensities.Rd:28-29: Dropping empty section \references
prepare_Rd: plotDensities.Rd:37-38: Dropping empty section \seealso
prepare_Rd: plotErrorBarsLines.Rd:35-36: Dropping empty section \details
prepare_Rd: plotErrorBarsLines.Rd:44-45: Dropping empty section \note
prepare_Rd: plotErrorBarsLines.Rd:42-43: Dropping empty section \author
prepare_Rd: plotErrorBarsLines.Rd:40-41: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:26-27: Dropping empty section \details
prepare_Rd: plotRelativeDensities.Rd:35-36: Dropping empty section \note
prepare_Rd: plotRelativeDensities.Rd:33-34: Dropping empty section \author
prepare_Rd: plotRelativeDensities.Rd:31-32: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:38-40: Dropping empty section \seealso
prepare_Rd: quantification.accuracy.Rd:7-9: Dropping empty section \description
prepare_Rd: quantification.accuracy.Rd:36-38: Dropping empty section \details
prepare_Rd: quantification.accuracy.Rd:50-52: Dropping empty section \note
prepare_Rd: quantification.accuracy.Rd:47-49: Dropping empty section \author
prepare_Rd: quantification.accuracy.Rd:44-46: Dropping empty section \references
prepare_Rd: quantification.accuracy.Rd:56-58: Dropping empty section \seealso
checkRd: (5) quantification.accuracy.Rd:0-79: Must have a \description
prepare_Rd: reliabilityCheckLibrary.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckLibrary.Rd:22-24: Dropping empty section \details
prepare_Rd: reliabilityCheckLibrary.Rd:34-36: Dropping empty section \note
prepare_Rd: reliabilityCheckLibrary.Rd:31-33: Dropping empty section \author
prepare_Rd: reliabilityCheckLibrary.Rd:28-30: Dropping empty section \references
prepare_Rd: reliabilityCheckLibrary.Rd:40-42: Dropping empty section \seealso
checkRd: (5) reliabilityCheckLibrary.Rd:0-54: Must have a \description
prepare_Rd: reliabilityCheckSwath.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckSwath.Rd:32-34: Dropping empty section \details
prepare_Rd: reliabilityCheckSwath.Rd:46-48: Dropping empty section \note
prepare_Rd: reliabilityCheckSwath.Rd:43-45: Dropping empty section \author
prepare_Rd: reliabilityCheckSwath.Rd:40-42: Dropping empty section \references
prepare_Rd: reliabilityCheckSwath.Rd:52-54: Dropping empty section \seealso
checkRd: (5) reliabilityCheckSwath.Rd:0-64: Must have a \description
prepare_Rd: swath.means.Rd:7-9: Dropping empty section \description
prepare_Rd: swath.means.Rd:22-24: Dropping empty section \details
prepare_Rd: swath.means.Rd:34-36: Dropping empty section \note
prepare_Rd: swath.means.Rd:31-33: Dropping empty section \author
prepare_Rd: swath.means.Rd:28-30: Dropping empty section \references
prepare_Rd: swath.means.Rd:40-42: Dropping empty section \seealso
checkRd: (5) swath.means.Rd:0-60: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
reliabilityCheckSwath   61.285  5.723  67.460
quantification.accuracy 11.332  2.217  14.058
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SwathXtend.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SwathXtend
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SwathXtend’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SwathXtend)

name	user	system	elapsed
applyttest	0.539	0.060	0.599
applyttestPep	0.495	0.012	0.508
buildSpectraLibPair	2.126	0.067	2.197
canonicalFormat	0.021	0.002	0.025
checkQuality	1.514	0.092	1.647
cleanLib	0.025	0.002	0.027
coverage	0.001	0.000	0.001
cv	0.001	0.000	0.001
fdr.crit	1.334	0.391	1.799
getFdrBins	3.494	1.032	4.697
medianNorm	0.025	0.002	0.028
mlr	0.009	0.001	0.010
mlrGroup	0.034	0.004	0.040
mlrrep	0.04	0.01	0.05
outputLib	0.073	0.008	0.081
plotAll	2.504	0.269	2.837
plotDensities	0.256	0.017	0.273
plotErrorBarsLines	0.006	0.000	0.005
plotRIICor	0.202	0.007	0.210
plotRTCor	1.555	0.048	1.603
plotRTResd	1.603	0.032	1.635
plotRelativeDensities	0.024	0.004	0.027
quantification.accuracy	11.332	2.217	14.058
readLibFile	0.027	0.001	0.029
reliabilityCheckLibrary	1.014	0.160	1.076
reliabilityCheckSwath	61.285	5.723	67.460
swath.means	1.210	0.379	1.659